Single Nucleotide Polymorphism‐Based Haplotypes Associated with Charcoal Rot Resistance in Brazilian Soybean Germplasm

Abstract

Core Ideas Incorporation of resistance to Charcoal Rot is an important goal for soybean breeding programs. Single nucleotide polymorphisms and haplotypes associated with Charcoal Rot resistance will be an important breeding component. Genome wide association studies that use haplotype information can afford new insights into the traits determinants. Incorporation of resistance to Charcoal Rot (CR), caused by the soil‐borne fungus Macrophomina phaseolina (Tassi) Goid., is an important goal for soybean [Glycine max (L.) Merr.] breeding programs. However, the limited accessible information on sources and hereditary mechanisms related to resistance has impeded progress, as reflected in the lack of commercial CR‐resistant soybean varieties around the world. The identification of single nucleotide polymorphisms (SNPs) and haplotypes associated with CR resistance will be an important breeding component. In this study, a genome wide association study (GWAS) was undertaken to identify genomic regions controlling CR resistance in a soybean association mapping panel, using single nucleotide polymorphism (SNP) markers and haplotype information. The soybean varieties (N = 169) were field‐evaluated on a site with a history of heavy CR infestation in Citrus Research Center and Agricultural Experiment Station (CRC‐AES) at the University of California, Riverside, USA, and genotyped with 6000 SNP markers. Symptoms of mortality were evaluated for 12 wk after the first symptoms of infection. Two SNP‐based haplotypes were found associated with CR in the genome‐wide haplotype association analysis. Two associations of stable haplotypes for CR, haplotype TAC and CGA of the markers Gm08_18909193_A_G, Gm08_44422211_T_C, and Gm19_34320762_A_C were identified. These markers are associated with other important disease resistance genes in the soybean genome. These findings will allow breeders to improve tropical soybean breeding for CR resistance. A haplotype‐based GWAS can provide more information into the genetic basis of CR resistance that could not be captured by the single marker approach.